From 5a4c39b73f1e89814ba82b0293cf8c5349faa117 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>
Date: Tue, 10 Jan 2023 11:31:12 +0100
Subject: [PATCH] fix: make GNU parallel more robust with --plain and --workdir
 (#328) (#331)

---
 snappy_wrappers/wrappers/bcftools/call_joint/wrapper.py    | 6 ++++++
 snappy_wrappers/wrappers/bcftools_call/wrapper.py          | 3 ++-
 snappy_wrappers/wrappers/gatk3_hc/wrapper.py               | 3 ++-
 snappy_wrappers/wrappers/gatk3_ug/wrapper.py               | 3 ++-
 snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py | 3 ++-
 snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py      | 3 ++-
 snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py         | 3 ++-
 snappy_wrappers/wrappers/varscan/call_joint/wrapper.py     | 3 +++
 8 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/snappy_wrappers/wrappers/bcftools/call_joint/wrapper.py b/snappy_wrappers/wrappers/bcftools/call_joint/wrapper.py
index 3dacb0015..b65bb2b86 100644
--- a/snappy_wrappers/wrappers/bcftools/call_joint/wrapper.py
+++ b/snappy_wrappers/wrappers/bcftools/call_joint/wrapper.py
@@ -48,11 +48,17 @@
 # Hack: get back bin directory of base/root environment.
 export PATH=$PATH:$(dirname $(dirname $(which conda)))/bin
 
+export TMPDIR=$(mktemp -d)
+trap "rm -rf $TMPDIR" EXIT
+mkdir -p $TMPDIR/parallel
+
 snappy-genome_windows \
     --fai-file $REF.fai \
     --window-size {snakemake.config[step_config][somatic_variant_calling][bcftools_joint][window_length]} \
     {args_ignore_chroms} \
 | parallel \
+    --plain \
+    --workdir $TMPDIR/parallel \
     --keep-order \
     --verbose \
     --max-procs {snakemake.config[step_config][somatic_variant_calling][bcftools_joint][num_threads]} \
diff --git a/snappy_wrappers/wrappers/bcftools_call/wrapper.py b/snappy_wrappers/wrappers/bcftools_call/wrapper.py
index 0a9b7ff79..914c7323d 100644
--- a/snappy_wrappers/wrappers/bcftools_call/wrapper.py
+++ b/snappy_wrappers/wrappers/bcftools_call/wrapper.py
@@ -125,9 +125,10 @@
 export -f run-shard
 
 # Perform parallel execution
+mkdir -p $TMPDIR/parallel
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_joint][num_threads]}
 cat $TMPDIR/final_intervals.txt \
-| parallel -j $num_threads 'run-shard {{#}} {{}}'
+| parallel --plain --workdir $TMPDIR/parallel -j $num_threads 'run-shard {{#}} {{}}'
 
 # Merge the individual shards' output VCF
 bcftools concat \
diff --git a/snappy_wrappers/wrappers/gatk3_hc/wrapper.py b/snappy_wrappers/wrappers/gatk3_hc/wrapper.py
index a4b6590c2..58701a8ef 100644
--- a/snappy_wrappers/wrappers/gatk3_hc/wrapper.py
+++ b/snappy_wrappers/wrappers/gatk3_hc/wrapper.py
@@ -108,9 +108,10 @@
 export -f run-shard
 
 # Perform parallel execution
+mkdir -p $TMPDIR/parallel
 num_threads={snakemake.config[step_config][variant_calling][gatk3_hc][num_threads]}
 cat $TMPDIR/final_intervals.txt \
-| parallel -j $num_threads 'run-shard {{#}} {{}}'
+| parallel --plain --workdir $TMPDIR/parallel -j $num_threads 'run-shard {{#}} {{}}'
 
 # Merge the individual shards' output VCF
 bcftools concat \
diff --git a/snappy_wrappers/wrappers/gatk3_ug/wrapper.py b/snappy_wrappers/wrappers/gatk3_ug/wrapper.py
index 71636ec86..52cc88fd7 100644
--- a/snappy_wrappers/wrappers/gatk3_ug/wrapper.py
+++ b/snappy_wrappers/wrappers/gatk3_ug/wrapper.py
@@ -109,9 +109,10 @@
 export -f run-shard
 
 # Perform parallel execution
+mkdir -p $TMPDIR/parallel
 num_threads={snakemake.config[step_config][variant_calling][gatk3_ug][num_threads]}
 cat $TMPDIR/final_intervals.txt \
-| parallel -j $num_threads 'run-shard {{#}} {{}}'
+| parallel --plain --workdir $TMPDIR/parallel -j $num_threads 'run-shard {{#}} {{}}'
 
 # Merge the individual shards' output VCF
 bcftools concat \
diff --git a/snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py
index f4630cb92..25e85cd10 100644
--- a/snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py
+++ b/snappy_wrappers/wrappers/gatk4_hc/combine_gvcfs/wrapper.py
@@ -110,9 +110,10 @@
 export -f run-shard
 
 # Perform parallel execution
+mkdir -p $TMPDIR/parallel
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_gvcf][num_threads]}
 cat $TMPDIR/final_intervals.txt \
-| parallel -j $num_threads 'run-shard {{#}} {{}}'
+| parallel --workdir $TMPDIR/parallel --plain -j $num_threads 'run-shard {{#}} {{}}'
 
 # Merge the individual shards' output VCF
 bcftools concat \
diff --git a/snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py
index e5eefc6a4..6167215cd 100644
--- a/snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py
+++ b/snappy_wrappers/wrappers/gatk4_hc/discover/wrapper.py
@@ -113,9 +113,10 @@
 export -f run-shard
 
 # Perform parallel execution
+mkdir -p $TMPDIR/parallel
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_gvcf][num_threads]}
 cat $TMPDIR/final_intervals.txt \
-| parallel -j $num_threads 'run-shard {{#}} {{}}'
+| parallel --workdir $TMPDIR/parallel --plain -j $num_threads 'run-shard {{#}} {{}}'
 
 # Merge the individual shards' output VCF
 bcftools concat \
diff --git a/snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py b/snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py
index f8a153656..e441ed9fb 100644
--- a/snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py
+++ b/snappy_wrappers/wrappers/gatk4_hc/joint/wrapper.py
@@ -111,9 +111,10 @@
 export -f run-shard
 
 # Perform parallel execution
+mkdir -p $TMPDIR/parallel
 num_threads={snakemake.config[step_config][variant_calling][gatk4_hc_joint][num_threads]}
 cat $TMPDIR/final_intervals.txt \
-| parallel -j $num_threads 'run-shard {{#}} {{}}'
+| parallel --plain --workdir $TMPDIR/parallel -j $num_threads 'run-shard {{#}} {{}}'
 
 # Merge the individual shards' output VCF
 bcftools concat \
diff --git a/snappy_wrappers/wrappers/varscan/call_joint/wrapper.py b/snappy_wrappers/wrappers/varscan/call_joint/wrapper.py
index e9bcc9af4..40f6c73da 100644
--- a/snappy_wrappers/wrappers/varscan/call_joint/wrapper.py
+++ b/snappy_wrappers/wrappers/varscan/call_joint/wrapper.py
@@ -108,9 +108,12 @@
 }}
 
 
+mkdir -p $TMPDIR/parallel
 for vartype in snp indel; do
     generate_intervals \
     | parallel \
+        --plain \
+        --workdir $TMPDIR/parallel
         --keep-order \
         --verbose \
         --max-procs {snakemake.config[step_config][somatic_variant_calling][varscan_joint][num_cores]} \